Sync wiki from main: single --out/--engine plotting, viewer GIFs, ASCII prose, updated benchmarks/figures
Perf: one headline (~970x end-to-end), drop warm-map multipliers; short Docker section
fetch Zenodo-only wording; plain Windows note; drop Docker/smoke; consolidate benchmark tables (1M threads×batch grid); custom-GTF stdout-only
Updated Installation (markdown)
Point testing docs at pytest, not the removed run_tests.py The monolithic tests/run_tests.py was migrated into the pytest suite, so update Installation/Architecture/FAQ to describe pytest (modules, golden files, --update-goldens) and the pip install -e + pytest -q run.
Restructure wiki into a sequential 7-section workflow Install -> Building an index -> Mapping -> Plotting -> Tutorials and notebooks -> Performance and benchmarking -> Reference. Merge the old scattered pages (Genome-onboarding + Custom-proteins -> Index; Output-modes + Input-format -> Mapping; Performance-and-RAM + Validation + Benchmarks -> Performance and benchmarking); drop the standalone Quickstart and CLI-reference. Update all CLI to the four-command form (index / map / fetch / plot) and the fetch-defaults-to-Zenodo model. Sidebar lists each section's subsections.
Initial wiki — 17 pages mirrored from main repo wiki/